Comparative coat protein annotation of two biologically distinct strains of cucumber mosaic virus in chili

Cucumber mosaic virus (CMV) is a globally prevalent plant virus with a broad host range, significantly affecting chili crops. From a diagnostic survey, 49 symptomatic chili plants were collected and CMV was confirmed in 23 samples. Molecular indexing revealed a predominance of mosaic-inducing strains (18 samples) along with distinct chlorosis inducing strains (5 samples) of CMV in the chili eco system of Tamil Nadu. Representative strains were mechanically sap inoculated onto chili host plants and produced similar symptoms as observed under field conditions. Coat protein (CP) gene analysis revealed 657 nucleotides encoding for 218 amino acids with a homology of 97.65 %–98.92 % with Indian chili isolates. Sequence diversity analysis indicated the higher synonymous substitutions in chlorosis-inducing strains, suggesting greater nucleotide variability. Comparative amino acid analysis indicated conserved residues in chlorosis-inducing strains such as Ser¹²⁹, Thr¹³⁷ and Thr¹⁶² and mosaic-inducing strains such as Pro¹²⁹, Ser¹³⁷ and Ala¹⁶². Furthermore, CP annotation performed by predicting secondary structures showed conformational modification in the loop structure of protein. To validate the symptomatology, in silico protein-protein docking was carried out to explore the possible interaction between chloroplast ferredoxin proteins of chili based on previous studies. Functional annotation substantiated that chlorotic symptom expression may be due to amino acid variation of Ser¹²⁹ and aids compatible interaction between chloroplast ferredoxin proteins of chili. These findings provide novel insights into the molecular basis of strain-specific symptom development and highlight the need for targeted diagnostics of emerging CMV variants in chili cultivation.